I am sorry about this, but I have a very, very strong opinion on pre 1968 F engines. They are a poor design and not even a simple valve job should be attempted on this block as it is wasted money. I had 23 (twenty three) trucks with this engine and 3 ran with the original engine, most had blown cranks or no engine at all (the engine died). I have seen ton's of other engines of that period that have punched holes in one or both sides of the block. I have thrown at least 12 other FJ40 '63-'67 engines in the Tucson dump. The last one I saw was in the local dump here with you guessed it- a 3" hole. Not too long ago online someone asked if Toyota LC engines were good as his dad's new 1966 blew the engine at 14K.
While some rebuild 1968-1973 F engines (aluminum intake manifold) I would only find a good used runner for $400 or less. The 2F engine is far better, parts can be found, and don't suffer from the known defects of earlier series. One of these should be found easily for $600 running w/o smoking etc. I spent $5,000 on a warranteed rebuild ('83 2F) from an east coast cruiser shop years ago and had problems in the warranty period (which the shop failed to cover) and after 27K the head failed. i would hesitate to have anyone repeat mistakes that can be avoided and even the cheap 'paclift kits' and your own labor cannot make up for this.
I bet i can guess the east coast shop that you're talking about...
As for the F engine, Rick is right, the later models are better, but for the same money, you can have a 2F.
When the F in my 71 blew (#2 cylinder cracker in half), i dropped a 79 motor into it. Wasn't too hard, had to fabricate a few little things, and it took some head scrtaching, but i did it by myself (as in ALONE) on a college budget with the most remedial of hand tools.